The objective of this study was to identify the effects of age and diet, with particular focus on carbohydrate and protein sources, on the colonic mucosa microbiota of dogs. Thirty-six healthy beagles were used in a 3x2 factorial design. Dogs were separated in 2 age groups, young adult (2.6 ± 0.9 yr) and geriatric (10.2 ± 1.1 yr), and were assigned to 3 isonutritive kibble dietary groups containing: (1) a non-fermentable insoluble fiber (IF; 34% poultry meal; 8% sugarcane fiber); (2) a fermentable fiber (FF; 35% poultry meal; 10% beet pulp); and (3) soybean meal (SM; 30% SM; 11% poultry meal; no additional fiber source). Dogs were fed the experimental diets for 30-d, followed by sample collection on d 31. Mucosal biopsies from the colon were performed by colonoscopy procedure with dogs under anesthesia. DNA was extracted and the V4 region of the 16S rRNA gene was amplified and subjected to Miseq Illumina sequencing. Data analysis was performed using QIIME 1.8.0. The resulting operational taxonomic units (OTU) were aligned to the Greengenes 13_8 database (97% similarity threshold). Firmicutes (44.1%) was the predominant bacterial phylum, followed by Bacteroidetes (39.2%), Fusobacteria (6.5%), Proteobacteria (5.6%), Actinobacteria (4.3%) and Deferribateres (0.2%). There was an interaction between age and diet (P < 0.05) for Prevotella, Sutterella, and an undefined genus in the Mogibacteriaceae family. The abundance of Slackia, Bacteriodes, Plesiomonas, and an undefined genus in the Paraprevotellaceae family were lower (P < 0.05) in geriatric dogs compared with the young adult dogs. Peptococcus and Slackia genus were in a higher (P < 0.05) abundance in dogs fed the IF and FF diets than those fed the SM diet. Dogs fed the IF diet had lower (P < 0.05) colonic mucosa Megamonas and Suturella abundance when compared with the dogs fed FF and SM diets. In conclusion, both dietary fiber fermentability and age may impact the microbial communities present on the colonic mucosa of dogs. More research is needed to identify the relevance of these microbial shifts in regards to gastrointestinal health.